> On Friday 17 December 2004 18:32, Bob Hanson wrote:
>> I take that back. It IS reproducible=21=21=21 See
>>
>> http://www.stolaf.edu/people/hansonr/tmp/wow.htm
>>
>> What a cool applet=21=21=21=21=21
>
> Does not work on Konqueror:
No version of Konqueror on any OS is supported.
It has severe bugs.
I have filed a detailed bug report with sample code demonstrating one of
the problems.
They have not yet responded (although it has only been a week or two).
Miguel

On Friday 17 December 2004 21:05, Bob Hanson wrote:
> Miguel: This needs looking into.
>
> Egon: What is "Konqueror"?
The KDE webbrowser... actually using the same code base as Safari... (or
actually the other way around...)
> Here's the full HTML code. Just very simple. Why would it be thinking this
> is Jme? Is it reading the initial lines incorrectly? Is Konqueror passing
> strange line terminators to the applet?
Likely a Konqueror bug... I'll post one.
Egon
--
egonw@...
GPG: 1024D/D6336BA6

Yes, that's it. I forgot the "scale" parameter. Probably should read my own
documentation.... Ah, but in the process I see there is an undocumented command:
vibration x
where x is the number of seconds to allow for one full vibration cycle.
OK, I'll get that one in there. Buy, hey, that WOW is fun. I say, leave it.
vector scale 1;vector 0.5
is what produces the effect.
Bob
Miguel wrote:
>>I take that back. It IS reproducible!!! See
>>
>>http://www.stolaf.edu/people/hansonr/tmp/wow.htm
>
>
> Doesn't work for me.
>
> But I can see the source code.
>
> You have 'vectors .5' ... just put 'vectors on' or 'vectors 3'
>
> No need to have 'animation on' ... in fact it probably will cause
> performance problems.
>
> 'vibration on' is what you want.
>
> Maybe what you were looking for was:
>
> 'vibration scale .5; vectors scale .5'
>
>
> Miguel
>
>
>>ps. Gotta fix this.....
>
>
> Not today :-)
>
>
>
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--
Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@...
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein

I wrote:
> Doesn't work for me.
My mistake ... it *does* work for me.
I broke my plugin when testing on different versions of the JVM.
Oh ... and it does look pretty wild :-O
Miguel
-----
Open Source Molecular Visualization
http://www.jmol.org
miguel=40jmol.org
-----

> I take that back. It IS reproducible=21=21=21 See
>
> http://www.stolaf.edu/people/hansonr/tmp/wow.htm
Doesn't work for me.
But I can see the source code.
You have 'vectors .5' ... just put 'vectors on' or 'vectors 3'
No need to have 'animation on' ... in fact it probably will cause
performance problems.
'vibration on' is what you want.
Maybe what you were looking for was:
'vibration scale .5; vectors scale .5'
Miguel
> ps. Gotta fix this.....
Not today :-)

Ah, it appears
vibration n
simply sets the SPEED of the vibration, not the magnitude.
NOW, it WOULD be nice to have the vibration speed as well, but magnitude is more
important....
and I can't get vectors working. So this must have to do with the vector business.
Bob
Miguel wrote:
> Bob asked:
>
>
>>Miguel, do you have a simple example of an xyz file that specifies
>>vibration vectors?
>
>
> Unfortunately not.
>
> There is a samples/xyz/cs2.xyz ... but I don't trust it ... I don't think
> it is correct.
>
> And the only way I would know how to create one is by looking at a
> gaussian file and creating the .xyz file by hand.
>
> Maybe someone else knows how to do this and could contribute a simple
> molecule with vibrations ...
>
>
> Miguel
>
>
>
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--
Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@...
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein

> I see it:
>
> http://cvs.sourceforge.net/viewcvs.py/*checkout*/jmol/Jmol/samples/xyz/=
cs2.xyz?rev=3D1.1
>
> That file is fine; just a pretty odd combination of vectors and
> coordinates.
> I put this in http://www.stolaf.edu/people/hansonr/jmol/inline/ and it =
did
> the
> job. I don't see what the middle column is for. It doesn't seem to be
> necessary.
I assume you mean the middle column of numbers in the .xyz file
That is supposed to be the formal charge.
> BUT
>
> WOW
>
> You have to see this screen shot. I don't think I'll be able to reprodu=
ce
> it.
> From the gif you can't appreciate the amazing animation. Everything is=
> flashing
> and moving back and forth. Totally awesome=21 Whatever could it be?
Perhaps it is that new type of 'antimatter' that I have been working on .=
..
> http://www.stolaf.edu/people/hansonr/tmp/wow.gif
Well, it *does* look interesting.
The Cone drawing code for the tops of the vectors gets very unhappy (and
breaks) if the cone is too flat.
It is a bug that will need to be fixed some day.
In this case, I suspect that you made the vectors 'oversquare', with the
diameter wider than the length.
vector 1.0
Or something like that.
Miguel

I take that back. It IS reproducible!!! See
http://www.stolaf.edu/people/hansonr/tmp/wow.htm
What a cool applet!!!!!
Bob
ps. Gotta fix this.....
Miguel wrote:
> Bob asked:
>
>
>>Miguel, do you have a simple example of an xyz file that specifies
>>vibration vectors?
>
>
> Unfortunately not.
>
> There is a samples/xyz/cs2.xyz ... but I don't trust it ... I don't think
> it is correct.
>
> And the only way I would know how to create one is by looking at a
> gaussian file and creating the .xyz file by hand.
>
> Maybe someone else knows how to do this and could contribute a simple
> molecule with vibrations ...
>
>
> Miguel
>
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> Jmol-developers mailing list
> Jmol-developers@...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@...
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein

I see it:
http://cvs.sourceforge.net/viewcvs.py/*checkout*/jmol/Jmol/samples/xyz/cs2.xyz?rev=1.1
That file is fine; just a pretty odd combination of vectors and coordinates.
I put this in http://www.stolaf.edu/people/hansonr/jmol/inline/ and it did the
job. I don't see what the middle column is for. It doesn't seem to be necessary.
BUT
WOW
You have to see this screen shot. I don't think I'll be able to reproduce it.
From the gif you can't appreciate the amazing animation. Everything is flashing
and moving back and forth. Totally awesome! Whatever could it be?
http://www.stolaf.edu/people/hansonr/tmp/wow.gif
supposedly from:
http://www.stolaf.edu/people/hansonr/tmp/wow.htm
Bob
Miguel wrote:
> Bob asked:
>
>
>>Miguel, do you have a simple example of an xyz file that specifies
>>vibration vectors?
>
>
> Unfortunately not.
>
> There is a samples/xyz/cs2.xyz ... but I don't trust it ... I don't think
> it is correct.
>
> And the only way I would know how to create one is by looking at a
> gaussian file and creating the .xyz file by hand.
>
> Maybe someone else knows how to do this and could contribute a simple
> molecule with vibrations ...
>
>
> Miguel
>
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> Jmol-developers mailing list
> Jmol-developers@...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@...
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein

Bob asked:
> Miguel, do you have a simple example of an xyz file that specifies
> vibration vectors?
Unfortunately not.
There is a samples/xyz/cs2.xyz ... but I don't trust it ... I don't think=
it is correct.
And the only way I would know how to create one is by looking at a
gaussian file and creating the .xyz file by hand.
Maybe someone else knows how to do this and could contribute a simple
molecule with vibrations ...
Miguel

Egon Willighagen wrote:
> http://wiki.jmol.org/ScriptAnimation
>
> Oliver, I've added a discussion section below. Can I make the ScriptAnimation
> page read only with ACL, while people can still edit
> ScriptAnimation/Discussion?
>
> Bob, I'll add a link to the examples later... but it would be cool to have the
> examples inline in the Wiki... but I'll have to think about that... are the
> examples in Excel too?
No, the examples are just small HTML files with one examples.js script referenced.
Bob
>
> Egon
>
--
Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@... http://www.stolaf.edu/people/hansonr

>Hello again,
> We used pmesh files to describe symmetry elements of simple molecules.
>Files were in general very small - 6 kb for a 100 points mesh, 2kb for a 26
>points mesh. For a wavefunction the resolution should probably be higher,
>and then the file will be heavier, but I didn't try this.
>
Wavefunctions, if complex, can sometimes have 20,000 points,
and compression is presumably less effective because unlike a plane,
there is no repetition.
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs@... (iChat)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK.
(Voracious anti-spam filter in operation for received email.
If expected reply not received, please phone/fax).

>>
>> I'm not an expert, but from what I understand, the "load pmesh" command
>> requires files that end with ".tmesh".
>
>OK ... seems strange to me ;-)
>
>>> Q: What is your timeframe for development/deployment of this website?
>>>
>>> This item is on the Jmol task list. I hope to implement it
>>> within the next 4 to 6 months.
Whilst surface display is highly important to several areas of chemistry,
I would flag one property of surfaces that might need attention, namely
the <size> of the resulting files.
We adopted 3dmf (another mesh like metaformat) for wavefunction display
a few years ago, but it only became viable to deploy it on the web after a
a games developer (Brian Greenstone) made his 3dmf optimizer available to the
community. This normally reduces the size of the 3dmf file from around
5-12 Mbytes to 400-600K.
I have no idea if pmesh files will suffer the same problem, but if no efficient
optimiser is available, I suspect 10 Mbyte data files will not be viable for
Web pages. There is another issue of course, and that is getting suitable programs
(e.g Gaussview, GAMESS, Chem3D, MacMolPlt etc etc) to support the
pmesh format (and in a perfect world, 3dmf => pmesh conversion would also
be nice).
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs@... (iChat)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK.
(Voracious anti-spam filter in operation for received email.
If expected reply not received, please phone/fax).

Thank you!
Inbal
-----Original Message-----
From: jmol-developers-admin@...
[mailto:jmol-developers-admin@...] On Behalf Of Miguel
Sent: Thursday, December 16, 2004 4:50 PM
To: jmol-developers@...
Subject: RE: [Jmol-developers] Load pmesh and load file in Jmol
>> Q: What is the difference between 'pmesh' and 'tmesh' ?
>>
>> Googling on those term turned up little more than Prof.
>> Johnston's page
>> mentioned above.
>
> I'm not an expert, but from what I understand, the "load pmesh" command
> requires files that end with ".tmesh".
OK ... seems strange to me ;-)
>> Q: What is your timeframe for development/deployment of this website?
>>
>> This item is on the Jmol task list. I hope to implement it
>> within the next 4 to 6 months.
>>
>
> We hope to finish our first version (without all the options) within this
> time frame. Will it be difficult to translate everything to Jmol once we
> have a version working with Chime?
A translation from Chime to Jmol should be straightforward.
I recommend that your team encapsulate the use of Chime by using
JavaScript functions. That is, do not put the <embed> tags for Chime and
for the buttons inline. Rather, write your own JavaScript subroutines
which output the HTML for these objects.
If you are able to do this, then you should be able to reimplement your
functions to call the Jmol.js JavaScript functions ... and everything
should work.
You and your team should feel free to contact me if you have any questions.
>> If you were in a position to help fund the development of this feature
>> then the priority could/would be raised.
>
> Wish I were...
OK
>>
>> An 'unsigned/untrusted' applet cannot read from the local file system.
>> That would be a security violation.
>>
>> Several people have requested a 'signed' Jmol applet that would allow
>> access to the local file system.
>
> Actually, this feature is even more important then the "load pmesh"
> option.
> I'll ask our team, but again, I doubt if I can fund anything...
OK
Miguel
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